should-get-tests/*.should-get: replace $VIDJIL_DIR/data by $VIDJIL_DATA

See #2611.

should-get-tests/*.should-get: replace $VIDJIL_DIR/data by $VIDJIL_DATA
See #2611.
880abf7d · Mathieu Giraud · 35525c10 · 880abf7d · 880abf7d · 880abf7d
Commit 880abf7d authored Sep 13, 2017 by Mathieu Giraud
70 changed files
--- a/algo/tests/should-get-tests/10-md5-data.should-get
+++ b/algo/tests/should-get-tests/10-md5-data.should-get
 !NO_LAUNCHER:
-!LAUNCH: (cd $VIDJIL_DIR/data ; md5sum *.fasta || md5 -r *.fasta)
+!LAUNCH: (cd $VIDJIL_DATA ; md5sum *.fasta || md5 -r *.fasta)

 $ Check md5 in data/
 1:985219d9156b6d9e8966807595beada3 Stanford_S22.fa

--- a/algo/tests/should-get-tests/ambiguous_representative.should-get
+++ b/algo/tests/should-get-tests/ambiguous_representative.should-get
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -r 1 -k 4 -w 20 -z 0 -c clones -V $VIDJIL_DIR/data/toy_V.fa -J $VIDJIL_DIR/data/toy_J.fa $VIDJIL_DIR/data/ambiguous_representative.fa
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -r 1 -k 4 -w 20 -z 0 -c clones -V $VIDJIL_DATA/toy_V.fa -J $VIDJIL_DATA/toy_J.fa $VIDJIL_DATA/ambiguous_representative.fa

 $ Short reads properly segmented
 1:SEG_+.* -> .* 4

--- a/algo/tests/should-get-tests/ambiguous_representative2.should-get
+++ b/algo/tests/should-get-tests/ambiguous_representative2.should-get
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -A -c clones -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DIR/data/test_representatives.fa
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -A -c clones -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DATA/test_representatives.fa

 $ Three clones should be found
 1:3 clones

--- a/algo/tests/should-get-tests/cdr3-stopcodon.should-get
+++ b/algo/tests/should-get-tests/cdr3-stopcodon.should-get
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -c segment -3 -g $VIDJIL_DIR/germline/homo-sapiens.g:TRG $VIDJIL_DIR/data/cdr3-stopcodon.fa
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -c segment -3 -g $VIDJIL_DIR/germline/homo-sapiens.g:TRG $VIDJIL_DATA/cdr3-stopcodon.fa
 !LOG: out/cdr3-stopcodon.vidjil

 $ Two identical junctions in JSON

--- a/algo/tests/should-get-tests/cgi-align.should-get
+++ b/algo/tests/should-get-tests/cgi-align.should-get
-!LAUNCH: export REQUEST_METHOD=POST ; export CONTENT_TYPE=test ; $LAUNCHER $VIDJIL_DIR/browser/cgi/align.cgi < $VIDJIL_DIR/data/msa.fa
+!LAUNCH: export REQUEST_METHOD=POST ; export CONTENT_TYPE=test ; $LAUNCHER $VIDJIL_DIR/browser/cgi/align.cgi < $VIDJIL_DATA/msa.fa

 $ no spurious info
 0: .* bp in .* sequences

--- a/algo/tests/should-get-tests/cgi-align2.should-get
+++ b/algo/tests/should-get-tests/cgi-align2.should-get
-!LAUNCH: export REQUEST_METHOD=POST ; export CONTENT_TYPE=test ; $LAUNCHER $VIDJIL_DIR/browser/cgi/align.cgi < $VIDJIL_DIR/data/msa2.fa
+!LAUNCH: export REQUEST_METHOD=POST ; export CONTENT_TYPE=test ; $LAUNCHER $VIDJIL_DIR/browser/cgi/align.cgi < $VIDJIL_DATA/msa2.fa

 $ no spurious info
 0: .* bp in .* sequences

--- a/algo/tests/should-get-tests/cgi-align3.should-get
+++ b/algo/tests/should-get-tests/cgi-align3.should-get
-!LAUNCH: export REQUEST_METHOD=POST ; export CONTENT_TYPE=test ; $LAUNCHER $VIDJIL_DIR/browser/cgi/align.cgi < $VIDJIL_DIR/data/msa3.fa
+!LAUNCH: export REQUEST_METHOD=POST ; export CONTENT_TYPE=test ; $LAUNCHER $VIDJIL_DIR/browser/cgi/align.cgi < $VIDJIL_DATA/msa3.fa

 $ no spurious info
 0: .* bp in .* sequences

--- a/algo/tests/should-get-tests/chimera-fake-2.should-get
+++ b/algo/tests/should-get-tests/chimera-fake-2.should-get
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -A -t 0 -g $VIDJIL_DIR/germline -2 $VIDJIL_DIR/data/chimera-fake.fa
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -A -t 0 -g $VIDJIL_DIR/germline -2 $VIDJIL_DATA/chimera-fake.fa

 $ The KmerSegmenter segments the three chimera reads on PSEUDO_MAX12 germline (-2)
 1:unexpected .* -> .* 3

--- a/algo/tests/should-get-tests/chimera-fake-D.should-get
+++ b/algo/tests/should-get-tests/chimera-fake-D.should-get
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -A -g $VIDJIL_DIR/germline -2 $VIDJIL_DIR/data/chimera-fake-D.fa
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -A -g $VIDJIL_DIR/germline -2 $VIDJIL_DATA/chimera-fake-D.fa

 $ The KmerSegmenter segments the chimera reads on PSEUDO_MAX12 germline (-2)
 f1:unexpected .* -> .* 2

--- a/algo/tests/should-get-tests/chimera-fake-VJ-germlines-trim.should-get
+++ b/algo/tests/should-get-tests/chimera-fake-VJ-germlines-trim.should-get
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -A -g $VIDJIL_DIR/data/chimera-fake-VJ-trim.g $VIDJIL_DIR/data/chimera-fake-VJ.fa
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -A -g $VIDJIL_DATA/chimera-fake-VJ-trim.g $VIDJIL_DATA/chimera-fake-VJ.fa
 # Testing a custom (fake) .g with special parameters for the algorithm

 $ The KmerSegmenter segments no read in Y because of the parameter

--- a/algo/tests/should-get-tests/chimera-fake-VJ-germlines.should-get
+++ b/algo/tests/should-get-tests/chimera-fake-VJ-germlines.should-get
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -A -g $VIDJIL_DIR/data/chimera-fake-VJ.g $VIDJIL_DIR/data/chimera-fake-VJ.fa
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -A -g $VIDJIL_DATA/chimera-fake-VJ.g $VIDJIL_DATA/chimera-fake-VJ.fa
 # Testing a custom (fake) germlines.data

 $ Report the species

--- a/algo/tests/should-get-tests/chimera-fake-VJ.should-get
+++ b/algo/tests/should-get-tests/chimera-fake-VJ.should-get
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -A -g $VIDJIL_DIR/germline -2 $VIDJIL_DIR/data/chimera-fake-VJ.fa
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -A -g $VIDJIL_DIR/germline -2 $VIDJIL_DATA/chimera-fake-VJ.fa

 $ The KmerSegmenter segments the five chimera reads on PSEUDO_MAX12 germline (-2)
 1:unexpected .* -> .* 5

--- a/algo/tests/should-get-tests/chimera-fake-half.should-get
+++ b/algo/tests/should-get-tests/chimera-fake-half.should-get
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -e 100 -A -t 0 -g $VIDJIL_DIR/germline -4 $VIDJIL_DIR/data/chimera-fake-half.fa
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -e 100 -A -t 0 -g $VIDJIL_DIR/germline -4 $VIDJIL_DATA/chimera-fake-half.fa
 # TODO: a more precise modeling should give a e-value computation that could make this work even with -e 1

 $ The KmerSegmenter segments the six chimera reads on PSEUDO_MAX1U germline (-4)

--- a/algo/tests/should-get-tests/chimera-fake.should-get
+++ b/algo/tests/should-get-tests/chimera-fake.should-get
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline $VIDJIL_DIR/data/chimera-fake.fa
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline $VIDJIL_DATA/chimera-fake.fa

 $ Do not segment on any germline, even incomplete
 1:junction detected in 0 reads

--- a/algo/tests/should-get-tests/chimera.should-get
+++ b/algo/tests/should-get-tests/chimera.should-get
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -A -uU -g $VIDJIL_DIR/germline $VIDJIL_DIR/data/chimera-trg.fa
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -A -uU -g $VIDJIL_DIR/germline $VIDJIL_DATA/chimera-trg.fa

 $ Do not segment on IGL by chance
 f1:IGL .* -> .* 0

--- a/algo/tests/should-get-tests/clones_lec.should-get
+++ b/algo/tests/should-get-tests/clones_lec.should-get
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline/homo-sapiens.g:TRG -c clones -A -3 $VIDJIL_DIR/data/segment_lec.fa
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline/homo-sapiens.g:TRG -c clones -A -3 $VIDJIL_DATA/segment_lec.fa

 $ Extract 50bp windows (TRG)
 1:found . 50-windows

--- a/algo/tests/should-get-tests/clones_simul.should-get
+++ b/algo/tests/should-get-tests/clones_simul.should-get
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -k 14 -w 50 -c clones -V $VIDJIL_DIR/germline/homo-sapiens/IGHV.fa -J $VIDJIL_DIR/germline/homo-sapiens/IGHJ.fa -y 3 -z 1 -r 1 $VIDJIL_DIR/data/clones_simul.fa
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -k 14 -w 50 -c clones -V $VIDJIL_DIR/germline/homo-sapiens/IGHV.fa -J $VIDJIL_DIR/germline/homo-sapiens/IGHJ.fa -y 3 -z 1 -r 1 $VIDJIL_DATA/clones_simul.fa

 $ Junction extractions
 1:found 25 50-windows in 66 reads

--- a/algo/tests/should-get-tests/clones_simul_cluster.should-get
+++ b/algo/tests/should-get-tests/clones_simul_cluster.should-get
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -k 14 -w 50 -c clones -V $VIDJIL_DIR/germline/homo-sapiens/IGHV.fa -J $VIDJIL_DIR/germline/homo-sapiens/IGHJ.fa -y 3 -z 0 -r 1 -n 5 $VIDJIL_DIR/data/clones_simul.fa ; cat out/clones_simul.vidjil
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -k 14 -w 50 -c clones -V $VIDJIL_DIR/germline/homo-sapiens/IGHV.fa -J $VIDJIL_DIR/germline/homo-sapiens/IGHJ.fa -y 3 -z 0 -r 1 -n 5 $VIDJIL_DATA/clones_simul.fa ; cat out/clones_simul.vidjil

 $ Window extractions
 2:found 25 50-windows in 66 reads

--- a/algo/tests/should-get-tests/common-V-D.should-get
+++ b/algo/tests/should-get-tests/common-V-D.should-get
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -KA -z 0 -s \\\\#\\\\#\\\\#\\\\#\\\\#-\\\\#\\\\#\\\\#\\\\#\\\\# -V $VIDJIL_DIR/germline/homo-sapiens/IGHV.fa -J $VIDJIL_DIR/germline/homo-sapiens/IGHJ.fa -D $VIDJIL_DIR/germline/homo-sapiens/IGHD.fa   $VIDJIL_DIR/data/common-V-D.fa  ; cat out/common-V-D.affects
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -KA -z 0 -s \\\\#\\\\#\\\\#\\\\#\\\\#-\\\\#\\\\#\\\\#\\\\#\\\\# -V $VIDJIL_DIR/germline/homo-sapiens/IGHV.fa -J $VIDJIL_DIR/germline/homo-sapiens/IGHJ.fa -D $VIDJIL_DIR/germline/homo-sapiens/IGHD.fa   $VIDJIL_DATA/common-V-D.fa  ; cat out/common-V-D.affects

 $ Segments the sequence
 1: SEG  .* -> .* 1 

--- a/algo/tests/should-get-tests/example_mouse.should-get
+++ b/algo/tests/should-get-tests/example_mouse.should-get
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -3 -c segment -g $VIDJIL_DIR/germline/mus-musculus.g $VIDJIL_DIR/data/example_mouse.fa
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -3 -c segment -g $VIDJIL_DIR/germline/mus-musculus.g $VIDJIL_DATA/example_mouse.fa

 $ Segment sequence on IGK
 1:segIGK.*IGKV.*IGKJ

--- a/algo/tests/should-get-tests/gzip.should-get
+++ b/algo/tests/should-get-tests/gzip.should-get
 !NO_LAUNCHER:
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DIR/data/clones_simul.fa > out-fa ;  $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH -b clones_simul $VIDJIL_DIR/data/clones_simul.fa.gz > out-fa-gz ; diff -s -I '\#' -I 'index' -I 'data/clones_simul' out-fa out-fa-gz ; echo 'Diff: '\\$?; wc -l out-fa-gz
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DATA/clones_simul.fa > out-fa ;  $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH -b clones_simul $VIDJIL_DATA/clones_simul.fa.gz > out-fa-gz ; diff -s -I '\#' -I 'index' -I 'data/clones_simul' out-fa out-fa-gz ; echo 'Diff: '\\$?; wc -l out-fa-gz

 $ Identical output
 1:Diff: 0

--- a/algo/tests/should-get-tests/large-N.should-get
+++ b/algo/tests/should-get-tests/large-N.should-get
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH -r 1 $VIDJIL_DIR/data/large_N.fa
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH -r 1 $VIDJIL_DATA/large_N.fa

 $ Find a huge insertion in the segmentation
 1:>clone-001.*/[ACGT]{100}
--- a/algo/tests/should-get-tests/multi-complete.should-get
+++ b/algo/tests/should-get-tests/multi-complete.should-get
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline $VIDJIL_DIR/data/multi-complete.fa
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline $VIDJIL_DATA/multi-complete.fa

 $ Segment all the seven reads
 1:junction detected in 7 reads

--- a/algo/tests/should-get-tests/multi-i-complete.should-get
+++ b/algo/tests/should-get-tests/multi-i-complete.should-get
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline $VIDJIL_DIR/data/multi-complete.fa
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline $VIDJIL_DATA/multi-complete.fa

 $ Segment all the seven reads
 1:junction detected in 7 reads

--- a/algo/tests/should-get-tests/multi-i-short.should-get
+++ b/algo/tests/should-get-tests/multi-i-short.should-get
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline $VIDJIL_DIR/data/multi-short.fa
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline $VIDJIL_DATA/multi-short.fa

 $ Segment all the seven reads
 1:junction detected in 7 reads

--- a/algo/tests/should-get-tests/multi-segment.should-get
+++ b/algo/tests/should-get-tests/multi-segment.should-get
-!LAUNCH: $VIDJIL_DIR/vidjil -c segment $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH,IGK,IGL $VIDJIL_DIR/data/multi-complete.fa ; cat out/multi-complete.vidjil | python $VIDJIL_DIR/tools/format_json.py -1
+!LAUNCH: $VIDJIL_DIR/vidjil -c segment $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH,IGK,IGL $VIDJIL_DATA/multi-complete.fa ; cat out/multi-complete.vidjil | python $VIDJIL_DIR/tools/format_json.py -1

 $ Segment the Ig recombinations
 1:IGH SEG

--- a/algo/tests/should-get-tests/multi-short-affects.should-get
+++ b/algo/tests/should-get-tests/multi-short-affects.should-get
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -r 5 -K -g $VIDJIL_DIR/germline/homo-sapiens.g:TRA,TRB,TRD,TRG,IGH,IGK,IGL $VIDJIL_DIR/data/multi-short.fa ; head -n 17 out/multi-short.affects
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -r 5 -K -g $VIDJIL_DIR/germline/homo-sapiens.g:TRA,TRB,TRD,TRG,IGH,IGK,IGL $VIDJIL_DATA/multi-short.fa ; head -n 17 out/multi-short.affects
 # Testing .affects output (-K)

 $ First sequence (TRA), display sequence

--- a/algo/tests/should-get-tests/multi-short.should-get
+++ b/algo/tests/should-get-tests/multi-short.should-get
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline/homo-sapiens.g:TRA,TRB,TRG,TRD,IGH,IGK,IGL $VIDJIL_DIR/data/multi-short.fa
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline/homo-sapiens.g:TRA,TRB,TRG,TRD,IGH,IGK,IGL $VIDJIL_DATA/multi-short.fa

 $ Segment all the seven reads
 1:junction detected in 7 reads

--- a/algo/tests/should-get-tests/multi-tiny-segment.should-get
+++ b/algo/tests/should-get-tests/multi-tiny-segment.should-get
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -c segment -g $VIDJIL_DIR/germline $VIDJIL_DIR/data/multi-tiny.fa
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -c segment -g $VIDJIL_DIR/germline $VIDJIL_DATA/multi-tiny.fa

 $ Do not segment any of the seven reads
 7:UNSEG

--- a/algo/tests/should-get-tests/overlap-stdout.should-get
+++ b/algo/tests/should-get-tests/overlap-stdout.should-get
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -c segment -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH -A $VIDJIL_DIR/data/overlap-d-j.fa | grep -v web | tail -4 | tr -d '\\\\n' | wc -c
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -c segment -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH -A $VIDJIL_DATA/overlap-d-j.fa | grep -v web | tail -4 | tr -d '\\\\n' | wc -c

 $ Exported sequence has all the bases
 1:116

--- a/algo/tests/should-get-tests/quality-json.should-get
+++ b/algo/tests/should-get-tests/quality-json.should-get
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -c clones -A -g $VIDJIL_DIR/germline/homo-sapiens.g:TRG -A  $VIDJIL_DIR/data/segment_lec.fq > /dev/null ; cat out/segment_lec.vidjil
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -c clones -A -g $VIDJIL_DIR/germline/homo-sapiens.g:TRG -A  $VIDJIL_DATA/segment_lec.fq > /dev/null ; cat out/segment_lec.vidjil

 $ Window
 1:"id": "GGGGTCTATTACTGTGCCACCTGGGCCTTATTATAAGAAACTCTTTGGCA"

--- a/algo/tests/should-get-tests/revcomp.should-get
+++ b/algo/tests/should-get-tests/revcomp.should-get
-!LAUNCH: $LAUNCHER $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -k 9 -V $VIDJIL_DIR/germline/homo-sapiens/IGHV.fa -J $VIDJIL_DIR/germline/homo-sapiens/IGHJ.fa  -K -c clones $VIDJIL_DIR/data/revcomp.fa ; grep 'X.X.X' out/revcomp.affects | sed 's/[^X]//g'  | sort -u ; grep '#>'  out/revcomp.affects | sed 's/.*SEG.../e-value:/' | cut -f 1 -d' '
+!LAUNCH: $LAUNCHER $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -k 9 -V $VIDJIL_DIR/germline/homo-sapiens/IGHV.fa -J $VIDJIL_DIR/germline/homo-sapiens/IGHJ.fa  -K -c clones $VIDJIL_DATA/revcomp.fa ; grep 'X.X.X' out/revcomp.affects | sed 's/[^X]//g'  | sort -u ; grep '#>'  out/revcomp.affects | sed 's/.*SEG.../e-value:/' | cut -f 1 -d' '

 $ Segments both reads, normal and reverse
 1:junction detected in 2 reads

--- a/algo/tests/should-get-tests/segment_S22.should-get
+++ b/algo/tests/should-get-tests/segment_S22.should-get
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH -c segment $VIDJIL_DIR/data/segment_S22.fa | grep '^>' ; cat out/segment_S22.vidjil | python $VIDJIL_DIR/tools/format_json.py -1
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH -c segment $VIDJIL_DATA/segment_S22.fa | grep '^>' ; cat out/segment_S22.vidjil | python $VIDJIL_DIR/tools/format_json.py -1

 $ First sequence Stanford
 #                            164        175                 195     203

--- a/algo/tests/should-get-tests/segment_simul.should-get
+++ b/algo/tests/should-get-tests/segment_simul.should-get
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -v -g $VIDJIL_DIR/germline -c segment $VIDJIL_DIR/data/segment_simul.fa | grep '^[>#]'
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -v -g $VIDJIL_DIR/germline -c segment $VIDJIL_DATA/segment_simul.fa | grep '^[>#]'


 $ First sequence, easy segmentation (no error, few deletions at the windows, small N)

--- a/algo/tests/should-get-tests/segmentation-D-read-number.should-get
+++ b/algo/tests/should-get-tests/segmentation-D-read-number.should-get
@@ -6,9 +6,9 @@
 # other reads. This is what is tested, we first put 10 sequences, then 5 and
 # finally just the sequence of interest alone.

-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -d -r 1 -w 60 -z 100 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DIR/data/buggy-D.fa; \
-$VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -d -r 1 -w 60 -z 100 -x 6 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DIR/data/buggy-D.fa;\
-$VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -d -r 1 -w 60 -z 100 -x 1 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DIR/data/buggy-D.fa
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -d -r 1 -w 60 -z 100 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DATA/buggy-D.fa; \
+$VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -d -r 1 -w 60 -z 100 -x 6 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DATA/buggy-D.fa;\
+$VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -d -r 1 -w 60 -z 100 -x 1 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DATA/buggy-D.fa

 $ Three times the same window
 3: TGTGCGGGATCTTCGTCCTCTTATCATAATAATGGTTTTTTGGCGGGGGAGTCATGGGGC

--- a/algo/tests/should-get-tests/sequences_of_interest.should-get
+++ b/algo/tests/should-get-tests/sequences_of_interest.should-get
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -e 10 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH -W ACCGGTATTACT -W CAGCTGCTCCCC -W TGGGCCACTC -W ATCAACGCTGGCAATGGTAACACTAAATATTCACAGAAGTTCCAGGGCAGAGTCACCATTACCAGGGACACATACGCGAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAAGACACGGCTCTGTATTACTGTGCGAGAGTGCGCAGCAGCTGGTCTGATGCTTTTGATTATCTGG $VIDJIL_DIR/data/clones_simul.fa
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -e 10 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH -W ACCGGTATTACT -W CAGCTGCTCCCC -W TGGGCCACTC -W ATCAACGCTGGCAATGGTAACACTAAATATTCACAGAAGTTCCAGGGCAGAGTCACCATTACCAGGGACACATACGCGAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAAGACACGGCTCTGTATTACTGTGCGAGAGTGCGCAGCAGCTGGTCTGATGCTTTTGATTATCTGG $VIDJIL_DATA/clones_simul.fa

 $ ACCGGTATTACT is found (in window and representative and in the command line)
 3:ACCGGTATTACT

--- a/algo/tests/should-get-tests/several-g.should-get
+++ b/algo/tests/should-get-tests/several-g.should-get
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline -g $VIDJIL_DIR/germline/homo-sapiens-isotypes.g $VIDJIL_DIR/data/isotypes.fa
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline -g $VIDJIL_DIR/germline/homo-sapiens-isotypes.g $VIDJIL_DATA/isotypes.fa

 $ Report the correct species
 1: Homo sapiens .9606.

--- a/algo/tests/should-get-tests/stanford-X100-sampled.should-get
+++ b/algo/tests/should-get-tests/stanford-X100-sampled.should-get
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -y 0 -X 100 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DIR/data/Stanford_S22.fasta
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -y 0 -X 100 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DATA/Stanford_S22.fasta

 $ Skip the good number of reads
 1:Processing every 131th read

--- a/algo/tests/should-get-tests/stanford-debug.should-get
+++ b/algo/tests/should-get-tests/stanford-debug.should-get
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -\# FA -k 16 -z 0 -w 60 -r 5 -o out2 -uuu -U -v -V $VIDJIL_DIR/germline/homo-sapiens/IGHV.fa -J $VIDJIL_DIR/germline/homo-sapiens/IGHJ.fa   $VIDJIL_DIR/data/Stanford_S22.fasta ; tail out2/Stanford_S22.segmented.vdj.fa ; grep UNSEG out2/Stanford_S22.unsegmented.vdj.fa
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -\# FA -k 16 -z 0 -w 60 -r 5 -o out2 -uuu -U -v -V $VIDJIL_DIR/germline/homo-sapiens/IGHV.fa -J $VIDJIL_DIR/germline/homo-sapiens/IGHJ.fa   $VIDJIL_DATA/Stanford_S22.fasta ; tail out2/Stanford_S22.segmented.vdj.fa ; grep UNSEG out2/Stanford_S22.unsegmented.vdj.fa
 # Testing uncommon and debug options 

 $ verbose (-v)

--- a/algo/tests/should-get-tests/stanford-detailed.should-get
+++ b/algo/tests/should-get-tests/stanford-detailed.should-get
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -z 2 -r 5 -a -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DIR/data/Stanford_S22.fasta ; cat out/seq/clone.fa-2
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -z 2 -r 5 -a -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DATA/Stanford_S22.fasta ; cat out/seq/clone.fa-2
 # Testing detailed clone output (-a)

 $ Detailed clone output (out/seq/clone.fa-2), germline

--- a/algo/tests/should-get-tests/stanford-fuse.should-get
+++ b/algo/tests/should-get-tests/stanford-fuse.should-get
 !REQUIRES: python $VIDJIL_DIR/tools/check_python_version.py
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -z 0 -w 60 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DIR/data/Stanford_S22.fasta ; python $VIDJIL_DIR/tools/fuse.py out/Stanford_S22.vidjil out/Stanford_S22.vidjil -o out/fused.data ; cat out/fused.data | python $VIDJIL_DIR/tools/format_json.py -1
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -z 0 -w 60 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DATA/Stanford_S22.fasta ; python $VIDJIL_DIR/tools/fuse.py out/Stanford_S22.vidjil out/Stanford_S22.vidjil -o out/fused.data ; cat out/fused.data | python $VIDJIL_DIR/tools/format_json.py -1

 $ Points list
 e1:"original_names": ["../../..//data/Stanford_S22.fasta", "../../..//data/Stanford_S22.fasta"]

--- a/algo/tests/should-get-tests/stanford-json.should-get
+++ b/algo/tests/should-get-tests/stanford-json.should-get
 !REQUIRES: python $VIDJIL_DIR/tools/check_python_version.py
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -3 -z 1 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH -w 60 -r 5 -e 10 -b data  $VIDJIL_DIR/data/Stanford_S22.fasta > /dev/null ; cat out/data.vidjil | python $VIDJIL_DIR/tools/format_json.py -1
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -3 -z 1 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH -w 60 -r 5 -e 10 -b data  $VIDJIL_DATA/Stanford_S22.fasta > /dev/null ; cat out/data.vidjil | python $VIDJIL_DIR/tools/format_json.py -1

 $ From homo-sapiens.g
 1:"ref": "http://www.vidjil.org/germlines/germline-.*.tar.gz"

--- a/algo/tests/should-get-tests/stanford-k14.should-get
+++ b/algo/tests/should-get-tests/stanford-k14.should-get
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -y 0 -k 14 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DIR/data/Stanford_S22.fasta
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -y 0 -k 14 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DATA/Stanford_S22.fasta
 !LOG: stanford-k14.log

 $ Find the good number of windows in Stanford S22 (contiguous seed 14)

--- a/algo/tests/should-get-tests/stanford-labels-FaW.should-get
+++ b/algo/tests/should-get-tests/stanford-labels-FaW.should-get
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -x 2000 -t 0 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH -FaW GAGAGGTTACTATGATAGTAGTGGTTATTACGGGGTAGGGCAGTACTACT $VIDJIL_DIR/data/Stanford_S22.fasta ; cat out/seq/clone.fa-1
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -x 2000 -t 0 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH -FaW GAGAGGTTACTATGATAGTAGTGGTTATTACGGGGTAGGGCAGTACTACT $VIDJIL_DATA/Stanford_S22.fasta ; cat out/seq/clone.fa-1

 $ Keep only one windows, the one given by -W, with only 2 reads in the first 2000 reads (it is actually the second clone in Stanford_S22.fasta)
 1: keep 1 windows in 2 reads

--- a/algo/tests/should-get-tests/stanford-labels-W.should-get
+++ b/algo/tests/should-get-tests/stanford-labels-W.should-get
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -x 100 -z 0 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH -r 5 -W ACTGTGCGAGAGTTGGAATTAGTAGTGGCTGGCCTGATTCCTGGGGCCAG $VIDJIL_DIR/data/Stanford_S22.fasta ; cat out/Stanford_S22.vidjil
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -x 100 -z 0 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH -r 5 -W ACTGTGCGAGAGTTGGAATTAGTAGTGGCTGGCCTGATTCCTGGGGCCAG $VIDJIL_DATA/Stanford_S22.fasta ; cat out/Stanford_S22.vidjil

 $ Some clone has only one read, bypassing the -r 5 option, and the good label
 1: clone-00..*0001-.* -W

--- a/algo/tests/should-get-tests/stanford-labels.should-get
+++ b/algo/tests/should-get-tests/stanford-labels.should-get
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -z 0 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH -x 100 -r 5 -l $VIDJIL_DIR/data/Stanford_S22.label $VIDJIL_DIR/data/Stanford_S22.fasta ; cat out/Stanford_S22.vidjil
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -z 0 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH -x 100 -r 5 -l $VIDJIL_DATA/Stanford_S22.label $VIDJIL_DATA/Stanford_S22.fasta ; cat out/Stanford_S22.vidjil

 $ Some clone has only one read, bypassing the -r 5 option, and the good label
 1: clone-00..*0001-.* my-clone

--- a/algo/tests/should-get-tests/stanford-segment-x100-first.should-get
+++ b/algo/tests/should-get-tests/stanford-segment-x100-first.should-get
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -c segment -x 2 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DIR/data/Stanford_S22.fasta
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -c segment -x 2 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DATA/Stanford_S22.fasta

 $ Segments the good number of sequences in Stanford S22 
 2: >lcl

--- a/algo/tests/should-get-tests/stanford-t1.should-get
+++ b/algo/tests/should-get-tests/stanford-t1.should-get
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -y 0 -t 1 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH -x 100 $VIDJIL_DIR/data/Stanford_S22.fasta
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -y 0 -t 1 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH -x 100 $VIDJIL_DATA/Stanford_S22.fasta

 $ No read segmented as we have no germline because of the -t
 1: UNSEG too few V/J ->      100
--- a/algo/tests/should-get-tests/stanford-vidjil-to-fasta.should-get
+++ b/algo/tests/should-get-tests/stanford-vidjil-to-fasta.should-get
 !REQUIRES: python $VIDJIL_DIR/tools/check_python_version.py
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -x 100 -r 1 -z 5 -w 60 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DIR/data/Stanford_S22.fasta ; python $VIDJIL_DIR/tools/vidjil-to-fasta.py  -o out/S22.fasta out/Stanford_S22.vidjil ;
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -x 100 -r 1 -z 5 -w 60 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DATA/Stanford_S22.fasta ; python $VIDJIL_DIR/tools/vidjil-to-fasta.py  -o out/S22.fasta out/Stanford_S22.vidjil ;
 !OUTPUT_FILE: out/S22.fasta

 $ 5 representative sequences in the FASTA output file

--- a/algo/tests/should-get-tests/stanford-w100.should-get
+++ b/algo/tests/should-get-tests/stanford-w100.should-get
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -e 10 -y 0 -s '#####-#####' -w 100 -V $VIDJIL_DIR/germline/homo-sapiens/IGHV.fa -D $VIDJIL_DIR/germline/homo-sapiens/IGHD.fa -J $VIDJIL_DIR/germline/homo-sapiens/IGHJ.fa $VIDJIL_DIR/data/Stanford_S22.fasta
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -e 10 -y 0 -s '#####-#####' -w 100 -V $VIDJIL_DIR/germline/homo-sapiens/IGHV.fa -D $VIDJIL_DIR/germline/homo-sapiens/IGHD.fa -J $VIDJIL_DIR/germline/homo-sapiens/IGHJ.fa $VIDJIL_DATA/Stanford_S22.fasta
 !LOG: stanford-w100.log

 $ Find the good number of "too short sequences" for windows of size 100

--- a/algo/tests/should-get-tests/stanford-wall.should-get
+++ b/algo/tests/should-get-tests/stanford-wall.should-get
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -w all -r 1 -y 15 -z 0 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DIR/data/Stanford_S22.fasta
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -w all -r 1 -y 15 -z 0 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DATA/Stanford_S22.fasta

 # Testing '-w all' option


--- a/algo/tests/should-get-tests/stanford-x100-first.should-get
+++ b/algo/tests/should-get-tests/stanford-x100-first.should-get
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -y 0 -x 100 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DIR/data/Stanford_S22.fasta
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -y 0 -x 100 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DATA/Stanford_S22.fasta

 $ Analyze the good number of sequences in Stanford S22 
 1: found .* of 100 reads
--- a/algo/tests/should-get-tests/stanford-xyz-yall.should-get
+++ b/algo/tests/should-get-tests/stanford-xyz-yall.should-get
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -r 1 -x 10 -y all -z 1 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DIR/data/Stanford_S22.fasta ; cat out/Stanford_S22.vdj.fa
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -r 1 -x 10 -y all -z 1 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DATA/Stanford_S22.fasta ; cat out/Stanford_S22.vdj.fa

 # Testing -x/-y/-z options


--- a/algo/tests/should-get-tests/stanford-xyz.should-get
+++ b/algo/tests/should-get-tests/stanford-xyz.should-get
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -r 1 -x 10 -y 5 -z 1 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DIR/data/Stanford_S22.fasta ; cat out/Stanford_S22.vdj.fa
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -r 1 -x 10 -y 5 -z 1 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DATA/Stanford_S22.fasta ; cat out/Stanford_S22.vdj.fa

 # Testing -x/-y/-z options


--- a/algo/tests/should-get-tests/stanford.should-get
+++ b/algo/tests/should-get-tests/stanford.should-get
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -e 10 -z 0 -V $VIDJIL_DIR/germline/homo-sapiens/IGHV.fa -D $VIDJIL_DIR/germline/homo-sapiens/IGHD.fa -J $VIDJIL_DIR/germline/homo-sapiens/IGHJ.fa -s \\\\#\\\\#\\\\#\\\\#\\\\#\\\\#-\\\\#\\\\#\\\\#\\\\#\\\\#\\\\# $VIDJIL_DIR/data/Stanford_S22.fasta
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -e 10 -z 0 -V $VIDJIL_DIR/germline/homo-sapiens/IGHV.fa -D $VIDJIL_DIR/germline/homo-sapiens/IGHD.fa -J $VIDJIL_DIR/germline/homo-sapiens/IGHJ.fa -s \\\\#\\\\#\\\\#\\\\#\\\\#\\\\#-\\\\#\\\\#\\\\#\\\\#\\\\#\\\\# $VIDJIL_DATA/Stanford_S22.fasta

 $ Germlines are custom
 1: custom germlines

--- a/algo/tests/should-get-tests/tools-align.should-get
+++ b/algo/tests/should-get-tests/tools-align.should-get
-!LAUNCH: $VIDJIL_DIR/algo/tools/align -m 6 -i 0 -j 1 $VIDJIL_DIR/data/msa.fa
+!LAUNCH: $VIDJIL_DIR/algo/tools/align -m 6 -i 0 -j 1 $VIDJIL_DATA/msa.fa

 $ Default cost and parameters
 1: (4, -6/-10/-10, -9999-9999/-9999-9999, -1, -2)

--- a/algo/tests/should-get-tests/tools-similarity.should-get
+++ b/algo/tests/should-get-tests/tools-similarity.should-get
-!LAUNCH: $VIDJIL_DIR/algo/tools/similarity $VIDJIL_DIR/data/msa.fa
+!LAUNCH: $VIDJIL_DIR/algo/tools/similarity $VIDJIL_DATA/msa.fa

 $ Read 3 sequences
 1: 54 bp in .* 3 sequences

--- a/algo/tests/should-get-tests/trb-only-VJ.should-get
+++ b/algo/tests/should-get-tests/trb-only-VJ.should-get
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -A -g $VIDJIL_DIR/germline/homo-sapiens.g:TRB $VIDJIL_DIR/data/trb-only-VJ.fa ; cat out/trb-only-VJ.vidjil
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -A -g $VIDJIL_DIR/germline/homo-sapiens.g:TRB $VIDJIL_DATA/trb-only-VJ.fa ; cat out/trb-only-VJ.vidjil

 $ Segments the read on TRB (the information is given twice, stdout + .vidjil)
 2: TRB .* -> .* 1

--- a/algo/tests/should-get-tests/trd-dd2-dd3-complete.should-get
+++ b/algo/tests/should-get-tests/trd-dd2-dd3-complete.should-get
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -A -g $VIDJIL_DIR/germline/homo-sapiens.g:TRD $VIDJIL_DIR/data/trd-dd2-dd3.fa
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -A -g $VIDJIL_DIR/germline/homo-sapiens.g:TRD $VIDJIL_DATA/trd-dd2-dd3.fa

 $ Segment only 2 reads, because we do not look for incomplete recombinations
 1:junction detected in 2 reads

--- a/algo/tests/should-get-tests/trd-dd2-dd3-incomplete.should-get
+++ b/algo/tests/should-get-tests/trd-dd2-dd3-incomplete.should-get
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -w 10 -e 10 -A -g $VIDJIL_DIR/germline $VIDJIL_DIR/data/trd-dd2-dd3.fa
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -w 10 -e 10 -A -g $VIDJIL_DIR/germline $VIDJIL_DATA/trd-dd2-dd3.fa

 $ Segment 5 reads, thanks to -i
 1:junction detected in 5 reads

--- a/algo/tests/should-get-tests/trd-dd2-dd3.should-get
+++ b/algo/tests/should-get-tests/trd-dd2-dd3.should-get
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -e 10 -k 8 -w 20 -V $VIDJIL_DIR/germline/homo-sapiens/TRDV.fa -V $VIDJIL_DIR/germline/homo-sapiens/TRDD2_upstream.fa -J $VIDJIL_DIR/germline/homo-sapiens/TRDD3_downstream.fa -J $VIDJIL_DIR/germline/homo-sapiens/TRDJ.fa $VIDJIL_DIR/data/trd-dd2-dd3.fa
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -e 10 -k 8 -w 20 -V $VIDJIL_DIR/germline/homo-sapiens/TRDV.fa -V $VIDJIL_DIR/germline/homo-sapiens/TRDD2_upstream.fa -J $VIDJIL_DIR/germline/homo-sapiens/TRDD3_downstream.fa -J $VIDJIL_DIR/germline/homo-sapiens/TRDJ.fa $VIDJIL_DATA/trd-dd2-dd3.fa

 $ Segment all 8 reads, thanks to TRDD2 and TRDD3
 1: junction detected in 8 reads .100..

--- a/algo/tests/should-get-tests/unsegmentation-causes-u.should-get
+++ b/algo/tests/should-get-tests/unsegmentation-causes-u.should-get
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline/homo-sapiens.g:TRA,TRB,TRD,TRG,IGH,IGK,IGL -u $VIDJIL_DIR/data/segmentation-2.fa ; cat ./out///segmentation-2.UNSEG_ambiguous.fa ; cat ./out///segmentation-2.UNSEG_too_few_V_J.fa
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline/homo-sapiens.g:TRA,TRB,TRD,TRG,IGH,IGK,IGL -u $VIDJIL_DATA/segmentation-2.fa ; cat ./out///segmentation-2.UNSEG_ambiguous.fa ; cat ./out///segmentation-2.UNSEG_too_few_V_J.fa

 $ The proper unsegmentation cause is given
 1: UNSEG too short   -> .* 1

--- a/algo/tests/should-get-tests/unsegmentation-causes.should-get
+++ b/algo/tests/should-get-tests/unsegmentation-causes.should-get
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline/homo-sapiens.g:TRA,TRB,TRD,TRG,IGH,IGK,IGL -uuu $VIDJIL_DIR/data/segmentation-2.fa ; cat out/segmentation-2.unsegmented.vdj.fa
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline/homo-sapiens.g:TRA,TRB,TRD,TRG,IGH,IGK,IGL -uuu $VIDJIL_DATA/segmentation-2.fa ; cat out/segmentation-2.unsegmented.vdj.fa

 $ Only one sequence is segmented, but it is too small for a window (too short w)
 1: junction detected in 1 reads

--- a/algo/tests/should-get-tests/vidjil-error-w-small.should-get
+++ b/algo/tests/should-get-tests/vidjil-error-w-small.should-get
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -x 1 -w -10 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DIR/data/Stanford_S22.fasta 2>&1
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -x 1 -w -10 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DATA/Stanford_S22.fasta 2>&1
 !EXIT_CODE: 1

 $ Error, too small -w

--- a/algo/tests/should-get-tests/vidjil-small-w.should-get
+++ b/algo/tests/should-get-tests/vidjil-small-w.should-get
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -x 100 -r 1 -y 1 -z 0 -w 10 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DIR/data/Stanford_S22.fasta 2>&1
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -x 100 -r 1 -y 1 -z 0 -w 10 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DATA/Stanford_S22.fasta 2>&1
 !OUTPUT_FILE: out/seq/clone.fa-1
 ### !EXIT_CODE: 1


--- a/algo/tests/should-get-tests/vidjil-warning-A.should-get
+++ b/algo/tests/should-get-tests/vidjil-warning-A.should-get
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -A -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DIR/data/toy_V.fa
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -A -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DATA/toy_V.fa

 $ Warning, -A
 1:WARNING

--- a/algo/tests/should-get-tests/vidjil-warning-z.should-get
+++ b/algo/tests/should-get-tests/vidjil-warning-z.should-get
 !NO_LAUNCHER:
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -z 200 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DIR/data/trd-dd2-dd3.fa
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -z 200 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DATA/trd-dd2-dd3.fa

 $ Warning, -z
 1:WARNING

--- a/algo/tests/should-get-tests/vidjil_long_segment.should-get
+++ b/algo/tests/should-get-tests/vidjil_long_segment.should-get
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DIR/data/long-segmentation.fa
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DATA/long-segmentation.fa

 $ Sequence should be segmented by k-mer segmenter
 e1:SEG_+ -> 1 
--- a/algo/tests/should-get-tests/vidjil_revcomp_VdJa.should-get
+++ b/algo/tests/should-get-tests/vidjil_revcomp_VdJa.should-get
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline/ -r 1 -c clones $VIDJIL_DIR/data/revcomp-VdJa.fa
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline/ -r 1 -c clones $VIDJIL_DATA/revcomp-VdJa.fa

 $ Just one window found
 1:==> found 1 ..-windows

--- a/algo/tests/should-get-tests/vidjil_revcomp_s22.should-get
+++ b/algo/tests/should-get-tests/vidjil_revcomp_s22.should-get
-!LAUNCH: $LAUNCHER $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -z 1 -k 9 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH -% 0.001 -r 2 -x 1000 -y 1 -c clones $VIDJIL_DIR/data/Stanford_S22.fasta | sed 's/--IGH--.*VDJ\\(.*\\).$/\\1/' | sed 's/IGH SEG_./IGH SEG_X/' > vidjil_s22.log && $LAUNCHER $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -z 1 -k 9 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH -% 0.001 -r 2 -x 1000 -y 1 -c clones $VIDJIL_DIR/data/Stanford_S22.rc.fasta | sed 's/--IGH--.*VDJ\\(.*\\).$/\\1/' |  sed 's/IGH SEG_./IGH SEG_X/' > vidjil_s22_rc.log && diff out/Stanford_S22{,.rc}.vidjil | grep GGG && diff vidjil_s22.log vidjil_s22_rc.log
+!LAUNCH: $LAUNCHER $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -z 1 -k 9 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH -% 0.001 -r 2 -x 1000 -y 1 -c clones $VIDJIL_DATA/Stanford_S22.fasta | sed 's/--IGH--.*VDJ\\(.*\\).$/\\1/' | sed 's/IGH SEG_./IGH SEG_X/' > vidjil_s22.log && $LAUNCHER $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -z 1 -k 9 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH -% 0.001 -r 2 -x 1000 -y 1 -c clones $VIDJIL_DATA/Stanford_S22.rc.fasta | sed 's/--IGH--.*VDJ\\(.*\\).$/\\1/' |  sed 's/IGH SEG_./IGH SEG_X/' > vidjil_s22_rc.log && diff out/Stanford_S22{,.rc}.vidjil | grep GGG && diff vidjil_s22.log vidjil_s22_rc.log
 !EXIT_CODE: 1

 $ Same number segmented